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HI, i've got a 97 explorer xlt 5speed.... here is the problem...
when you start the truck and start driving... its making a Loud clunking noise from under the car... at first we thought it was the gear box but then after replacing with a reconditioned gearbox and transfer case it was still there... it is doing this in auto mode and in 4x4 mode... during city driving it does it all the time .... but when you drive it to 100km/h the clunking completely stops.... and then you can bring the car to a complete halt (without turning the engine off) and start driving again and the clunking is still gone... BUT as soon as you turn the engine off and on again (even if only for a minute) the clunking returns again until you drive to 100km/h and then it stops again.
well that shift motor isn't all the way in... the three screws that hold the casing on are missing and theres about a 5mm gap... it its only being held on by the bracket that is holding the end of the casing. i've tried removing it completely to see if it makes any difference... but none.
Do you still have the original transfer case? If so, can you use the screws from the old case to hold the shift motor in? Did the new transmission and transfer case may any improvement?
I'll also suggest you drain the front and rear differential fluids and see if there is any sign that the gears are not meshed correctly or have other issues (fluid will have a grey sparkly tint to it).
Is the noise only present when the vehicle is moving with no hints of the noise parked at idle? Are you pretty sure the noise isn't parking brake shoes that have come free from the backing plates? I'm not totally sure this would create a noise that goes away at high speed and doesn't come back until the vehicle has sat some amount of time.
I have repaired this problem several times in most situations it is the rear differential the noise comes up the drive shaft and sounds like the transmission.
It can also be the front differential there is generally a small leak on the input shaft in either case.
You should also address the transfer case problem also.
The cheap and relatively easy check might still be to pull the rear brake rotors and see if there is brake shoe lining material floating around. And if there is it still may not be the source of this noise, but would be probably the cheapest thing to try and yet not be a waste of time.